run_de: Runs differential expression for a ser object

In Chris-Cherry/sctools: Single cell analysis tools package

Description

Creates object used in make_de_plots function for the creation of various plots. Can be used on whole data set or individual clusters.

Usage

run_de(
  ser,
  feats = NULL,
  out_dir = "2_de/",
  meta = NULL,
  origin = "Condition",
  verbose = F
)

Arguments

ser	The Seurat object to use
feats	A subset of featurs to run DE (I.E. only surface markers) If NULL then will run on all genes
out_dir	Directory to write plots and save markers.
meta	(Optional) Pass in cluster name that user wants to run DE
origin	(Optional) Pass in what parameters in the each clusters that user wants to run DE
verbose	Boolean flag for verbose output

Value

Output a processed differential expression for plotting

Chris-Cherry/sctools documentation built on Jan. 25, 2022, 2:19 p.m.